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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3579_neuroectodermal_basal_amygdala_putamen_mesodermal_caudate_brain
|full_id=C3579_neuroectodermal_basal_amygdala_putamen_mesodermal_caudate_brain
|id=C3579
|id=C3579

Revision as of 16:31, 12 September 2012


Full id: C3579_neuroectodermal_basal_amygdala_putamen_mesodermal_caudate_brain



Phase1 CAGE Peaks

Hg19::chr16:62070305..62070310,-p4@CDH8
Hg19::chr16:62070317..62070352,-p1@CDH8
Hg19::chr16:62070355..62070364,-p3@CDH8


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
regional part of nervous system9.58e-4594
nervous system9.58e-4594
central nervous system6.86e-4482
neurectoderm5.94e-4290
neural tube6.16e-4157
neural rod6.16e-4157
future spinal cord6.16e-4157
neural keel6.16e-4157
neural plate1.88e-3886
presumptive neural plate1.88e-3886
regional part of brain4.95e-3759
brain4.09e-3569
future brain4.09e-3569
regional part of forebrain3.92e-3341
forebrain3.92e-3341
future forebrain3.92e-3341
anterior neural tube6.61e-3242
ectoderm3.14e-31173
presumptive ectoderm3.14e-31173
telencephalon1.32e-2834
gray matter1.35e-2834
brain grey matter1.35e-2834
pre-chordal neural plate1.42e-2861
ectoderm-derived structure1.84e-28169
regional part of telencephalon8.90e-2833
cerebral hemisphere3.55e-2732
adult organism5.27e-24115
head8.32e-22123
anterior region of body1.61e-21129
craniocervical region1.61e-21129
cerebral cortex5.80e-2125
pallium5.80e-2125
regional part of cerebral cortex5.37e-1922
neocortex3.57e-1720
tube1.79e-12194
organism subdivision1.86e-11365
posterior neural tube5.08e-1015
chordal neural plate5.08e-1015
multi-cellular organism5.49e-10659
cell layer8.82e-10312
epithelium1.41e-09309
basal ganglion2.24e-099
nuclear complex of neuraxis2.24e-099
aggregate regional part of brain2.24e-099
collection of basal ganglia2.24e-099
cerebral subcortex2.24e-099
nucleus of brain4.70e-099
neural nucleus4.70e-099
anatomical conduit8.69e-09241
segmental subdivision of nervous system1.03e-0813
segmental subdivision of hindbrain7.20e-0812
hindbrain7.20e-0812
presumptive hindbrain7.20e-0812
embryo1.35e-07612
telencephalic nucleus1.63e-077
anatomical cluster5.09e-07286
organ part5.17e-07219
multi-tissue structure9.60e-07347


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.